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haplotype analysis

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https://www.readbyqxmd.com/read/28530509/genotyping-toxoplasma-gondii-with-the-b1-gene-in-naturally-infected-sheep-from-an-endemic-region-in-the-pacific-coast-of-mexico
#1
Williams Arony Martínez-Flores, José Manuel Palma-García, Heriberto Caballero-Ortega, Alejandra Del Viento-Camacho, Eduardo López-Escamilla, Fernando Martínez-Hernández, Pablo Vinuesa, Dolores Correa, Pablo Maravilla
Toxoplasma gondii is a protozoan parasite with a broad ecological valence, which has been detected in a wide range of hosts and landscapes. Although the genus is considered monospecific, in recent years it has been demonstrated to exhibit more genetic variability than previously known. In Mexico, there are few genotyping studies, which suggest that classical, autochthonous, and atypical strains are circulating. The goal of this study was to describe T. gondii genetic diversity in naturally infected sheep from Colima, Mexico...
May 22, 2017: Vector Borne and Zoonotic Diseases
https://www.readbyqxmd.com/read/28530463/association-of-il-6-174-g-c-polymorphism-with-the-risk-of-sle-among-south-indians-evidence-from-case-control-study-and-meta-analysis
#2
S K Katkam, L Rajasekhar, K Kumaraswami, V K Kutala
Cytokines play a direct role in disease pathogenesis of systemic lupus erythematosus (SLE). Elevated levels of serum IL-6 are well documented with the disease activity and anti-dsDNA antibodies in SLE. The 5' promoter region of the IL-6 gene has been shown to play a significant role in the regulation of gene expression. In view of this, the current study aimed to investigate the possible association of 5' promoter polymorphisms G-597A (rs1800797), G-572C (rs1800796) and G-174C (rs1800795) with the risk of SLE...
January 1, 2017: Lupus
https://www.readbyqxmd.com/read/28527291/haplotypes-in-ccr5-ccr2-ccl3-and-ccl5-are-associated-with-natural-resistance-to-hiv-1-infection-in-a-colombian-cohort
#3
Jorge A Vega, Simón Villegas-Ospina, Wbeimar Aguilar-Jiménez, María T Rugeles, Gabriel Bedoya, Wildeman Zapata
INTRODUCTION: Variants in genes encoding for HIV-1 co-receptors and their natural ligands have been individually associated to natural resistance to HIV-1 infection. However, the simultaneous presence of these variants has been poorly studied. OBJECTIVE: To evaluate the association of single and multilocus haplotypes in genes coding for the viral co-receptors CCR5 and CCR2, and their ligands CCL3 and CCL5, with resistance or susceptibility to HIV-1 infection. MATERIALS AND METHODS: Nine variants in CCR5-CCR2, two SNPs in CCL3 and two in CCL5 were genotyped by PCR-RFLP in 35 seropositive (cases) and 49 HIV-1-exposed seronegative Colombian individuals (controls)...
June 1, 2017: Biomédica: Revista del Instituto Nacional de Salud
https://www.readbyqxmd.com/read/28527282/-determination-of-hla-a-b-and-drb1-polymorphism-in-brain-dead-organ-donors-representative-of-the-colombian-general-population-2007-2014
#4
Yazmin Rocío Arias, Karime Osorio-Arango, Brayan Bayona, Guadalupe Ercilla, Mauricio Beltrán-Durán
INTRODUCTION: Genes encoding for human leukocyte antigens (HLA) are highly polymorphic and of great importance in organ transplantation procedures, as determining allelic frequencies in defined populations is taken into account among the scientific criteria for organ allocation. OBJECTIVE: The objective of this study was to establish the antigen HLA-A, -B, and -DRB1 haplotype frequencies in organ donors representative of the Colombian population after brain death...
June 1, 2017: Biomédica: Revista del Instituto Nacional de Salud
https://www.readbyqxmd.com/read/28527106/a-trans-acting-factor-may-modify-age-at-onset-in-familial-amyloid-polyneuropathy-attrv30m-in-portugal
#5
Miguel Alves-Ferreira, Teresa Coelho, Diana Santos, Jorge Sequeiros, Isabel Alonso, Alda Sousa, Carolina Lemos
Although all familial amyloid polyneuropathy (FAP) ATTRV30M patients carry the same causative mutation, early (<40) and late-onset forms (≥50 years) of FAP may coexist in the same family. However, this variability in age at onset is still unexplained. To identify modifiers closely linked to the TTR locus that may in part be associated with age at onset of FAP ATTRV30M, in particular in a group of very early-onset patients (≤30 years) when compared with late-onset individuals. A clinical genetic study at a referral center comprising a sample of 910 Portuguese individuals includes 589 Val30Met carriers, 102 spouses, and 189 controls from the general population...
May 19, 2017: Molecular Neurobiology
https://www.readbyqxmd.com/read/28526729/phased-genotyping-by-sequencing-enhances-analysis-of-genetic-diversity-and-reveals-divergent-copy-number-variants-in-maize
#6
Heather Manching, Subhajit Sengupta, Keith R Hopper, Shawn W Polson, Yuan Ji, Randall J Wisser
High-throughput sequencing of reduced representation genomic libraries has ushered in an era of genotyping-by-sequencing (GBS), where genome-wide genotype data can be obtained for nearly any species. However, there remains a need for imputation-free GBS methods for genotyping large samples taken from heterogeneous populations of heterozygous individuals. This requires a number of issues encountered with GBS be considered, including the sequencing of non-overlapping sets of loci across multiple GBS libraries, a common missing data problem that results in low call rates for markers per individual, and a tendency for applicability only in inbred line samples with sufficient linkage disequilibrium for accurate imputation...
May 19, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28525980/the-distribution-of-mitochondrial-dna-haplogroup-h-in-southern-iberia-indicates-ancient-human-genetic-exchanges-along-the-western-edge-of-the-mediterranean
#7
Candela L Hernández, Jean M Dugoujon, Andrea Novelletto, Juan N Rodríguez, Pedro Cuesta, Rosario Calderón
BACKGROUND: The structure of haplogroup H reveals significant differences between the western and eastern edges of the Mediterranean, as well as between the northern and southern regions. Human populations along the westernmost Mediterranean coasts, which were settled by individuals from two continents separated by a relatively narrow body of water, show the highest frequencies of mitochondrial haplogroup H. These characteristics permit the analysis of ancient migrations between both shores, which may have occurred via primitive sea crafts and early seafaring...
May 19, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28525660/polymorphism-of-mitochondrial-dna-in-the-brazilian-canind%C3%A3-goat-breed
#8
N M V Silva, E C Pimenta Filho, J K G Arandas, M A Gomes Filho, E Ferreira, I Del Cerro, C Fonseca, M N Ribeiro
The success of the geographical distribution of goat populations around the world is a consequence of the adaptive potential of these breeds. Several relevant traits to the success of the species in colonizing different ecosystems (and use by man) evolved before domestication. These features were relevant for the selection of different breeds. Each breed represents a genetic heritage that may be unique and essential for maintaining the species. The objective of this study was to catalog the mtDNA haplotypes of the Brazilian autochthonous Canindé goat breed and to characterize the genetic diversity observed in subpopulations by sequencing a 481-bp fragment corresponding to the first portion of the control region in 178 individuals from 10 herds, sampled in six Brazilian states...
May 18, 2017: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28525570/droplet-barcode-sequencing-for-targeted-linked-read-haplotyping-of-single-dna-molecules
#9
David Redin, Erik Borgström, Mengxiao He, Hooman Aghelpasand, Max Käller, Afshin Ahmadian
Data produced with short-read sequencing technologies result in ambiguous haplotyping and a limited capacity to investigate the full repertoire of biologically relevant forms of genetic variation. The notion of haplotype-resolved sequencing data has recently gained traction to reduce this unwanted ambiguity and enable exploration of other forms of genetic variation; beyond studies of just nucleotide polymorphisms, such as compound heterozygosity and structural variations. Here we describe Droplet Barcode Sequencing, a novel approach for creating linked-read sequencing libraries by uniquely barcoding the information within single DNA molecules in emulsion droplets, without the aid of specialty reagents or microfluidic devices...
May 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28524827/impact-of-human-leukocyte-antigen-loci-and-haplotypes-on-intestinal-acute-graft-versus-host-disease-after-human-leukocyte-antigen-matched-sibling-peripheral-blood-stem-cell-transplantation
#10
Fa-Hong Yan, Mei Wang, Jian-Feng Yao, Er-Lie Jiang, Ming-Zhe Han
BACKGROUND: Acute graft-versus-host disease (aGVHD) is a common and severe complication of allogeneic hematopoietic stem cell transplantation (allo-HSCT). Some studies have found that the presence of certain specific human leukocyte antigen (HLA) loci could affect the occurrence of aGVHD. Meanwhile, the impact of HLA haplotypes on aGVHD has been rarely studied. This study aimed to investigate the effects of HLA loci and haplotypes on intestinal aGVHD. METHODS: Totally, 345 consecutive patients undergoing first HLA-matched sibling peripheral blood stem cell transplantation (PBSCT) from February 2004 to June 2013 at Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, were enrolled in this study...
June 5, 2017: Chinese Medical Journal
https://www.readbyqxmd.com/read/28524717/first-molecular-evidence-of-mus-musculus-bactrianus-in-nepal-inferred-from-the-mitochondrial-dna-cytochrome-b-gene-sequences
#11
Pradeep Adhikari, Sang-Hyun Han, Yoo-Kyung Kim, Tae-Wook Kim, Tej Bahadur Thapa, Naresh Subedi, Prabhat Adhikari, Hong-Shik Oh
To identify the house mice collected in Pokhara and Lumbini of Nepal at the subspecies level, morphological and molecular analyses were carried out. Morphologically, two populations collected in Pokhara and Lumbini were distinguished by fur colour, but there was no significant difference in external measurements (p > .05). The phylogenetic analysis results revealed that the haplotypes sequences of mitochondrial DNA (mtDNA) Cytochrome B (CytB) gene distinguished into two distinct clades on a phylogenetic tree representing two subspecies, Mus musculus bactrianus and M...
May 19, 2017: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/28521293/determination-of-il-1b-rs16944-and-il-6-rs1800796-genetic-polymorphisms-in-iga-nephropathy-in-a-northwest-chinese-han-population
#12
Daofa Zhang, Maowei Xie, Xiaohong Yang, Yin Zhang, Yan Su, Yanni Wang, Haiyang Huang, Hui Han, Wenning Li, Keying Fu, Huiluan Su, Wentan Xu, Yeguang Han, Ru Wang, Pei Zhang, Wei Wu, Yun Huang, Daojun Chen, Tianbo Jin, Jiali Wei
IgA nephropathy (IgAN) is the most common form of primary glomerulonephritis worldwide, but etiology and pathogenesis continue to be poorly understood. Polymorphisms in the cytokine genes may play a role in the etiology and pathogenesis of IgAN. The incidence of different between diverse ethnic groups suggested important genetic influences on its pathogenesis.We genotype 10 single nucleotide polymorphisms (SNPs) in IL-1B and IL-6 gene using Sequenom Mass-ARRAY technology from 417 IgAN patients and 463 healthy controls of the Chinese Han population...
May 4, 2017: Oncotarget
https://www.readbyqxmd.com/read/28518213/relationship-between-toll-like-receptor-2-r753q-and-t16934a-polymorphisms-and-staphylococcus-aureus-nasal-carriage
#13
Maciej Żukowski, Olga Taryma-Leśniak, Mariusz Kaczmarczyk, Katarzyna Kotfis, Łukasz Szydłowski, Andrzej Ciechanowicz, Mirosław Brykczyński, Agnieszka Żukowska
BACKGROUND: The association among specific single-nucleotide polymorphisms (SNPs) in TLR2 R753Q (rs5743708) and T16934A (rs4696480) and the nasal carriage of Staphylococcus aureus was studied in adults before CABG. METHODS: The TLR2 polymorphisms were genotyped in 299 consecutive patients prepared for a CABG operation. Genotyping was performed using restriction fragment length polymorphism (RFLP) analysis of PCR-amplified fragments. Two nasal swab cultures were taken within 2 weeks before the operation...
May 18, 2017: Anaesthesiology Intensive Therapy
https://www.readbyqxmd.com/read/28515913/promoter-polymorphisms-of-the-vascular-endothelial-growth-factor-gene-are-associated-with-metabolic-syndrome-susceptibility-in-koreans
#14
Young Ree Kim, Seung-Ho Hong
Vascular endothelial growth factor (VEGF) is a potent regulator of angiogenesis. Patients with metabolic syndrome (MetS) have elevated plasma VEGF levels. The aim of the present study was to investigate the association between promoter polymorphisms (the -2578C>A and -1154G>A) of the VEGF gene and MetS susceptibility. A total of 640 subjects were enrolled in the study including 320 patients with MetS and 320 healthy controls. Genotyping of the VEGF single nucleotide polymorphisms was performed by polymerase chain reaction-restriction fragment length polymorphism analysis...
May 2017: Biomedical Reports
https://www.readbyqxmd.com/read/28515435/genetic-diversity-of-armored-scales-hemiptera-diaspididae-and-soft-scales-hemiptera-coccidae-in-chile
#15
P Amouroux, D Crochard, J-F Germain, M Correa, J Ampuero, G Groussier, P Kreiter, T Malausa, T Zaviezo
Scale insects (Sternorrhyncha: Coccoidea) are one of the most invasive and agriculturally damaging insect groups. Their management and the development of new control methods are currently jeopardized by the scarcity of identification data, in particular in regions where no large survey coupling morphological and DNA analyses have been performed. In this study, we sampled 116 populations of armored scales (Hemiptera: Diaspididae) and 112 populations of soft scales (Hemiptera: Coccidae) in Chile, over a latitudinal gradient ranging from 18°S to 41°S, on fruit crops, ornamental plants and trees...
May 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28514720/new-application-for-haplotype-specific-extraction-separation-of-mitochondrial-dna-mixtures
#16
J Zander, J Rothe, J Dapprich, M Nagy
A particularly challenging aspect of forensic casework is the accurate interpretation of samples that contain DNA from more than one contributor, since DNA analysis of specific identification markers often results in ambiguous mixed profiles. Physically separating the various haploid components of a diploid or polyploid DNA sample or of a specimen containing DNA from multiple individuals can resolve this problem. We adapted and combined previously developed methods of haplotype-specific extraction (HSE) to separate and analyze mitochondrial DNA (mtDNA) in samples containing DNA from two individuals...
May 6, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28513770/association-between-mfn2-gene-polymorphisms-and-the-risk-and-prognosis-of-acute-liver-failure-a-case-control-study-in-a-chinese-population
#17
Y-L Wei, Q Tian, X-X Zhao, G-Z Qiu, Y Xu
This study aimed to determine the role of mitofusin 2 (MFN2) gene polymorphisms in the risk and prognosis of acute liver failure (ALF). A total of 298 blood samples were collected from 138 ALF patients (case group) and 160 healthy participants (control group). Coagulation function, glutamic pyruvic transaminase (GPT), glutamic oxaloacetic transaminase (GOT), total bilirubin (TB), blood ammonia and lactic acid (LA) were measured. The predictive evaluation of MFN2 gene polymorphisms in the risk and prognosis of ALF patients was estimated using Kaplan-Meier survival analysis, haplotype analysis, binary logistic regression analysis and Cox regression analysis...
May 15, 2017: Brazilian Journal of Medical and Biological Research, Revista Brasileira de Pesquisas Médicas e Biológicas
https://www.readbyqxmd.com/read/28511025/co-inheritance-of-the-membrane-frizzled-related-protein-ocular-phenotype-and-glycogen-storage-disease-type-ib
#18
Maha Mameesh, Anuradha Ganesh, Beena Harikrishna, Sana Al Zuhaibi, Patrick Scott, Sami Al Kalbani, Khalid Al Thihli
AIM: To report co-occurrence of two rare recessive conditions, the membrane frizzled-related protein (MFRP)-related ocular phenotype and glycogen storage disease type 1b (GSD-1b), in three siblings in an Omani family. BACKGROUND: Biallelic mutations in the MFRP gene (chromosome 11q23) result in a distinct ocular phenotype characterized by retinitis pigmentosa, foveoschisis, optic nerve head drusen, and posterior microphthalmos. GSD-1b is an autosomal-recessive disorder caused by mutations in SLC37A4 gene located in the same chromosomal region...
May 16, 2017: Ophthalmic Genetics
https://www.readbyqxmd.com/read/28508933/genetic-variants-within-key-nodes-of-the-cascade-of-antipsychotic-mechanisms-effects-on-antipsychotic-response-and-schizophrenia-psychopathology-in-a-naturalistic-treatment-setting-in-two-independent-korean-and-italian-samples
#19
Marco Calabrò, Stefano Porcelli, Concetta Crisafulli, Sheng-Min Wang, Soo-Jung Lee, Changsu Han, Ashwin A Patkar, Prakash S Masand, Diego Albani, Ilaria Raimondi, Gianluigi Forloni, Sofia Bin, Alessandro Mattiaccio, Vilma Mantovani, Tae-Youn Jun, Chi-Un Pae, Alessandro Serretti
INTRODUCTION: Schizophrenia (SCZ) is one of the most disabling psychiatric disorders. Genetic factors play an important role in both SCZ liability and its treatment outcome. In the present paper, we investigated the effects of several single nucleotide polymorphisms (SNPs) within ten strong candidate genes involved with antipsychotics (APs) mechanisms of action. METHODS: Two independent samples were investigated in the present study. Totals of 176 SCZ subjects and 326 controls of Korean ancestry, and 83 SCZ subjects and 194 controls of Italian ancestry were recruited and genotyped...
May 16, 2017: Advances in Therapy
https://www.readbyqxmd.com/read/28508507/detecting-selection-signatures-between-duroc-and-duroc-synthetic-pig-populations-using-high-density-snp-chip
#20
Z Edea, J-K Hong, J-H Jung, D-W Kim, Y-M Kim, E-S Kim, S S Shin, Y C Jung, K-S Kim
The development of high throughput genotyping techniques has facilitated the identification of selection signatures of pigs. The detection of genomic selection signals in a population subjected to differential selection pressures may provide insights into the genes associated with economically and biologically important traits. To identify genomic regions under selection, we genotyped 488 Duroc (D) pigs and 155 D × Korean native pigs (DKNPs) using the Porcine SNP70K BeadChip. By applying the FST and extended haplotype homozygosity (EHH-Rsb) methods, we detected genes under directional selection associated with growth/stature (DOCK7, PLCB4, HS2ST1, FBP2 and TG), carcass and meat quality (TG, COL14A1, FBXO5, NR3C1, SNX7, ARHGAP26 and DPYD), number of teats (LOC100153159 and LRRC1), pigmentation (MME) and ear morphology (SOX5), which are all mostly near or at fixation...
May 16, 2017: Animal Genetics
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